I can find out if the compounds I have in a list belong to an organism using Keggrest.

list_of_compounds = list(c('C00001', 'C00002', 'C00003', 'C00004'))

get_compound_belongs_to <- function(compound) {
  url <- paste('https://www.genome.jp/dbget-bin/www_bget?-f+m+cpd:', compound, sep="")
  page <- read_html(url)
  node <- html_node(page, '#pathway_tab_1 > ul > li > a')
  text <- html_text(node)
  return(text)
}

get_compound_belongs_to(list_of_compounds)